mmg_233_2013_genetics_genomicswikiaorg-20200214-history
Metagenomic analysis of the Porites astreoides coral microbiome
Corals are animals in the phylum Cnidaria. A coral is made of many individual animals called polyps that grow on a hard substrate and secrete calcium carbonate creating an individial calcium carbonate reef (1).Porites astreoides is a colonial coral that lives in shallow water reefs in the western Atlantic and Caribbean sea (2). This type of coral is also called mustard hill coral due to its yellow color (Figure 1). The color is provided by the algae zooxanthellae (Symbiodinium) living symbiotically with the coral polyps (2). In addition, the photosynthetic zooxanthellae produces glucose and amino acids that the coral polyps use to grow and survive (3). Under times of stress however, the polyps will expel the algae cells and the coral reef becomes white--also known as coral bleaching (4) (Figure 2). If the bleaching occurs for long periods of time the coral animal will die, leaving only the hard calcium carbonate exoskeleton. Therefore, the symbiotic relationship between the coral, algae symbionts and bacteria is especially important for the growth and development of not only the single polyp, but the reef ecosystem in general. Coral Microbiome Coral reefs are a diverse ecosystem of eukaryotic and prokaryotic organisms. Zooxanthellae are by far the most understood symbionts in the system. There appears to be a diverse subset of zooxanthellae algae that associate not only with coral but also clams and sea sponges (5). It is now known that 4 clades of this algae associate with corals, all showing variable stress resistance to light (Clade A), cold (Clade B), and sedimentation (Clade D). The stress tolerance of this symbiont could explain why some corals are more susceptible to bleaching while others appear resistant (5). In a hypothesis by Buddemeier and Fautin (5), corals expel zooxanthellae under stress in order to aquire adapted new zooxanthellae when the stress period is over. In addition to zooxanthellae, bacteria also contribute to the coral microbiome. Bacteria can be either helpful or detrimental to the corals. In the former, bacteria can scavenge nutrients and fix nitrogen for use by the coral. Detrimentally however, bacteria have been known to cause disease is sea fan corals (5). Metagenomic Analysis Given the mutualistic abilities of both zooxanthellae and bacteria, Wegley et al studied the specific microbial community in Porites astreoides coral (6). Notably, the coral micrbiome is comprised of the coral animal, algae, fungi, zooxanthellae, Bacteria, Archaea, and even viruses. In order to determine the metagenome, the authors homogenized pieces of P. astreoides obtained from Panama, extracted DNA, and sequenced the DNA using Pyrosequencing. Figure 3 shows the work flow associated with determining the metagenome of this coral species. Coral results metagenomics.jpg|Figure 4. Metagenomic Analysis of P. Astreoides. Metagenomic analysis determined many species associated in the coral microbiome. Picture adapted from Wegley et al. Coral Function.jpg|Figure 5. Function of Bacteria Associated with P. astreoides. All bacteria may be beneficial in providing needed metabolic activities to the coral. Picture adapted from Wegley et al. Coral virsus.jpg|Figure 6. Viral association to P. astreoides. Comparison of viruses that affect the coral in general versus the reef water. Picture adapted from Wegley et al. Of the microorganisms found associated with P. astreoides, 49% of the sequences were mitochondrial, 38% were fungi, 7% Bacteria, 3% phage, 2% eukaryotic viruses, and 1%'' Arachaea''. Sequences were compared using the SEED database (SEED non-redundant database), GenBANK (virus), SCUMS (phage), and RDP (Ribosomal database project). This data is noted in Figure 4. Of the Bacteria found, the authors classified the sequences in functional groups generating a chart wheel of the functional potential of the organisms found (Figure 5). The majority of the sequences found were for metabolism of sugars and proteins, aiding the coral in the breakdown of amino acids. Additionally, Figure 6 shows a summary of the viruses found associated with P. astreoides. These viruses were mostly viruses that infect coral reef fish, indicating a resevoir type function for P. astreoides. Results and Conclusions The final results of the metagenome analysis are summarized in Figure 7. The study by Wegley et al. was instrumental in determining the microbiome of a specific type of coral, P. astreoides. The information obtained helped to establish a role for coral-associated microbes and how stress to that biome may affect the overall health of the coral reef. References 1. Corals. Wikipedia. http://en.wikipedia.org/wiki/Coral 2. Porites asteriodes. Wikipedia. http://en.wikipedia.org/wiki/Porites_astreoides 3. National Oceanic and Atmospheric Administration. Zooxanthellae. http://oceanservice.noaa.gov/education/kits/corals/coral02_zooxanthellae.html 4. Coral Bleaching. Wikipedia. http://en.wikipedia.org/wiki/Coral_bleaching 5. Rohwer and Knowlton. "Multispecies Microbial Mutualism on Coral Reefs: The Host as a Habitat." The American Naturalist. Volume 162, No. S4, October 2003 PMID: 14583857 6. Wegley et al. "Metagenomic analysis of the microbial community associated with the coral Porites astreoides." Environmental Microbiology. (2007). 9(11), 2707-2719